[Bioperl-l] Entrez Gene ASN parsers

Stefan Kirov skirov at utk.edu
Sat Mar 12 17:59:16 EST 2005

I looked at the code (EntrezGene) and so far it seems to me it gives as 
you claim pretty accurate and easy to understand data structure (few 
dead entries and some 0 size array, but nothing major).
The only concern I have is that the data structure. If you want to 
achieve a better structure (non-redundant, two level where possible or a 
collection of Bioperl objects) this will slow things down. I guess I 
will compare how the code I wrote compares to yours and choose the 
faster one. I think this makes sense.

Liu, Mingyi wrote:

>I have just released a project on sourceforge that contains 4 different parsers for Entrez Gene ASN file based on regex, Parse::RecDescent, Parse::Yapp, and Perl-byacc.  They differ in performance and the regex-based parser is the best performer, processing over 13000 records a minute on average (It finishes the 900+ MB human annotation file in 11 minutes on one Intel Xeon 2.4 GHz CPU).  The other parsers are at least a few fold slower but I included them since it'd be of intererst to people learning to use those tools or choosing among the tools for a practical project.  All parsers are short OO-modules (<100 lines if not counting POD/YACC-generated code), so they are easy to use and understand.
>Right now my parsers do not assemble data into Bioperl objects (because for my project I only needed to put them into a proprietary XML format, which is not released (not that it's anything special, just IP issues.  Without IP issues, I could've released the parser code in Feb.)).  They behave like XML-parsers, namely, they parse entrez gene records and assemble content into data structures only.  But I hope it could serve as a base that Bioperl objects can be built (the data structure is easy to use).  Please feel free to use the code for any Bioperl or other projects as I released them under GPL (thanks to my company and a collaborating company's consent).
>Please also feel free to contact me if you have any suggestion or bug report.
>The URL for the sourceforge project is http://sourceforge.net/projects/egparser/
>Dr. Mingyi Liu
>Computational Biologist
>GPC Biotech Inc.
>610 Lincoln St.
>Waltham, MA 02451
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org

Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
5700 bldg, PO BOX 2008 MS6164
Oak Ridge TN 37831-6164
tel +865 576 5120
fax +865-576-5332
e-mail: skirov at utk.edu
sao at ornl.gov

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